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Merged
merged 2 commits into from
Nov 15, 2017
Merged

Name pre pro arg #101

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f97bfae
Move channelsToProcess to optional argument
ablot Nov 14, 2017
6a45331
Update calls of preProcessTiles
ablot Nov 14, 2017
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13 changes: 5 additions & 8 deletions code/preProcessTiles/preProcessTiles.m
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
function varargout=preProcessTiles(sectionsToProcess,channelsToProcess, varargin)
function varargout=preProcessTiles(sectionsToProcess, varargin)
% Load each tile and perform all calculations needed for subsequent quick stitching
%
% function analysesPerformed=preProcessTiles(sectionsToProcess,combCorChans,'param1',val1, ...)
Expand Down Expand Up @@ -38,12 +38,12 @@
% these section directories AND we over-write existing coefficient files in all
% channels.
%
%
% INPUTS (optional param/value pairs)
% - channelsToProcess - If is empty (default), all channels are
% used to generate tileStats files. If 0, only channels from
% `combCorChans` and/or `illumChans` will be processed.
%
%
% INPUTS (optional param/value pairs)
% - combCorChans - zero by default. combCorChans can be a scalar or
% a vector defining which image channels are to be *averaged together* for the
% comb correction. e.g. if it is [1,2], then we will average channels 1 and 2
Expand Down Expand Up @@ -103,19 +103,16 @@
sectionsToProcess=0;
end


if nargin<2
channelsToProcess=[];
end

params = inputParser;
params.CaseSensitive = false;
params.addParamValue('combCorChans', 0, @(x) isnumeric(x));
params.addParamValue('illumChans', 0, @(x) isnumeric(x));
params.addParamValue('channelsToProcess', 0, @(x) isnumeric(x));
params.addParamValue('verbose', true, @(x) islogical(x) || x==0 || x==1);
params.parse(varargin{:});

combCorChans=params.Results.combCorChans;
channelsToProcess=params.Results.channelsToProcess;
illumChans=params.Results.illumChans;
verbose=params.Results.verbose;

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2 changes: 1 addition & 1 deletion code/processDuringAcquistion/syncAndCrunch.m
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Expand Up @@ -328,7 +328,7 @@ function syncAndCrunch(localDir,serverDir,combCorChans,illumChans,chanToPlot)



analysesPerformed = preProcessTiles(0,0,'combCorChans', combCorChans, ...
analysesPerformed = preProcessTiles(0,'combCorChans', combCorChans, ...
'illumChans', illumChans); %PRE-PROCESS TILES


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2 changes: 1 addition & 1 deletion code/stitching/stitchAllChannels.m
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Expand Up @@ -84,7 +84,7 @@ function stitchAllChannels(chansToStitch,stitchedSize,illumChans,combChans)

%Loop through and stitch all requested channels
generateTileIndex; %Ensure the tile index is present
analysesPerformed = preProcessTiles(0,combChans,illumChans); %Ensure we have the pre-processing steps done
analysesPerformed = preProcessTiles(0, 'combChans', combChans,'illumChans', illumChans); %Ensure we have the pre-processing steps done

if analysesPerformed.illumCor || ~exist(fullfile(config.subdir.rawDataDir, config.subdir.averageDir),'dir');
collateAverageImages
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